Mercurial > repos > yating-l > hubarchivecreator
comparison BigWig.py @ 0:f493979f1408 draft default tip
planemo upload for repository https://github.com/Yating-L/hubarchivecreator-test commit 48b59e91e2dcc2e97735ee35d587960cbfbce932-dirty
| author | yating-l |
|---|---|
| date | Wed, 21 Dec 2016 12:13:04 -0500 |
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| children |
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| -1:000000000000 | 0:f493979f1408 |
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| 1 #!/usr/bin/python | |
| 2 | |
| 3 import os | |
| 4 import shutil | |
| 5 | |
| 6 # Internal dependencies | |
| 7 from Datatype import Datatype | |
| 8 from Track import Track | |
| 9 from TrackDb import TrackDb | |
| 10 | |
| 11 | |
| 12 class BigWig( Datatype ): | |
| 13 def __init__(self, input_bigwig_path, data_bigwig): | |
| 14 super(BigWig, self).__init__() | |
| 15 | |
| 16 self.track = None | |
| 17 | |
| 18 self.input_bigwig_path = input_bigwig_path | |
| 19 self.name_bigwig = data_bigwig["name"] | |
| 20 self.priority = data_bigwig["order_index"] | |
| 21 self.track_color = data_bigwig["track_color"] | |
| 22 # TODO: Think about how to avoid repetition of the group_name everywhere | |
| 23 self.group_name = data_bigwig["group_name"] | |
| 24 | |
| 25 #print "Creating TrackHub BigWig from (falsePath: %s; name: %s)" % ( self.input_bigwig_path, self.name_bigwig ) | |
| 26 | |
| 27 trackName = "".join( ( self.name_bigwig, ".bigwig" ) ) | |
| 28 | |
| 29 myBigWigFilePath = os.path.join(self.myTrackFolderPath, trackName) | |
| 30 shutil.copy(self.input_bigwig_path, myBigWigFilePath) | |
| 31 | |
| 32 # Create the Track Object | |
| 33 self.createTrack(file_path=trackName, | |
| 34 track_name=trackName, | |
| 35 long_label=self.name_bigwig, | |
| 36 track_type='bigWig', visibility='full', | |
| 37 priority=self.priority, | |
| 38 track_file=myBigWigFilePath, | |
| 39 track_color=self.track_color, | |
| 40 group_name=self.group_name) | |
| 41 | |
| 42 # dataURL = "tracks/%s" % trackName | |
| 43 # | |
| 44 # # Return the BigBed track | |
| 45 # | |
| 46 # trackDb = TrackDb( | |
| 47 # trackName=trackName, | |
| 48 # longLabel=self.name_bigwig, | |
| 49 # shortLabel=self.getShortName( self.name_bigwig ), | |
| 50 # trackDataURL=dataURL, | |
| 51 # trackType='bigWig', | |
| 52 # visibility='full', | |
| 53 # priority=self.priority, | |
| 54 # ) | |
| 55 # | |
| 56 # self.track = Track( | |
| 57 # trackFile=myBigWigFilePath, | |
| 58 # trackDb=trackDb, | |
| 59 # ) | |
| 60 | |
| 61 print("- BigWig %s created" % self.name_bigwig) | |
| 62 #print("- %s created in %s" % (trackName, myBigWigFilePath)) |